Variant report

Variant	rs12436216
Chromosome Location	chr14:35809414-35809415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:35757408..35763930-chr14:35809319..35813404,11	MCF-7	breast:
2	chr14:35783009..35785578-chr14:35809337..35811839,2	MCF-7	breast:
3	chr14:35801529..35804372-chr14:35808012..35809578,2	K562	blood:
4	chr14:35589885..35593973-chr14:35809162..35812137,5	MCF-7	breast:
5	chr14:35808792..35810743-chr14:35815553..35817945,2	K562	blood:
6	chr14:35592944..35595456-chr14:35809160..35811582,2	K562	blood:
7	chr14:35681682..35685352-chr14:35808762..35812906,3	MCF-7	breast:
8	chr14:35801529..35803038-chr14:35808078..35809983,2	K562	blood:
9	chr14:35801385..35810310-chr14:35830739..35838852,15	K562	blood:
10	chr14:35793707..35796135-chr14:35808509..35811220,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258790	Chromatin interaction
ENSG00000100902	Chromatin interaction
ENSG00000092020	Chromatin interaction
ENSG00000265530	Chromatin interaction
ENSG00000100890	Chromatin interaction
ENSG00000258860	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10083375	0.96[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10083387	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10132397	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10135277	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10136627	0.81[EUR][1000 genomes]
rs10140133	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10140922	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs10146008	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10146017	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10148567	0.84[EUR][1000 genomes]
rs10162508	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1040840	0.80[JPT][hapmap]
rs10438062	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12385925	0.85[EUR][1000 genomes]
rs12586302	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs1885151	0.90[ASN][1000 genomes]
rs2006074	0.98[ASN][1000 genomes]
rs2006075	0.93[ASN][1000 genomes]
rs2415275	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs28589517	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28627414	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2899835	0.98[ASN][1000 genomes]
rs4981283	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs4981285	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4981288	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs4982250	0.80[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.84[TSI][hapmap]
rs4982255	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4982258	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4982259	0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4982260	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4982261	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4982262	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4982265	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4982267	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs4982268	0.84[EUR][1000 genomes]
rs55746125	0.90[ASN][1000 genomes]
rs57645874	0.81[EUR][1000 genomes]
rs57856432	0.82[EUR][1000 genomes]
rs58519555	0.84[EUR][1000 genomes]
rs60049741	0.82[EUR][1000 genomes]
rs72666622	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72666634	0.84[EUR][1000 genomes]
rs762010	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8003074	0.92[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9322947	0.95[ASN][1000 genomes]
rs9322950	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949617	chr14:35379923-35825436	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv870305	chr14:35488290-35852349	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1053604	chr14:35548276-35825805	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1052392	chr14:35563220-35893309	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
5	nsv542036	chr14:35563220-35893309	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
6	nsv456205	chr14:35772940-35826370	ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv564318	chr14:35772940-35826370	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv1829386	chr14:35789740-35845927	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv518090	chr14:35802483-35840241	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12436216	NKX2-1	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35800000-35815000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr14:35800600-35814400	Enhancers	Placenta	Placenta
3	chr14:35800800-35812200	Enhancers	Fetal Thymus	thymus
4	chr14:35800800-35813800	Enhancers	Lung	lung
5	chr14:35801000-35810400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr14:35801400-35810200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr14:35802800-35810200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr14:35803000-35810400	Enhancers	Liver	Liver
9	chr14:35804600-35810800	Enhancers	Esophagus	oesophagus
10	chr14:35805800-35821000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr14:35806000-35810200	Enhancers	Adipose Nuclei	Adipose
12	chr14:35806200-35812400	Enhancers	Ovary	ovary
13	chr14:35806400-35810600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr14:35806400-35810800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr14:35806600-35810000	Weak transcription	Fetal Heart	heart
16	chr14:35806600-35810200	Weak transcription	Brain Anterior Caudate	brain
17	chr14:35806800-35810400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr14:35806800-35816200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr14:35806800-35816600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr14:35807000-35810000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr14:35807000-35810200	Weak transcription	Fetal Kidney	kidney
22	chr14:35807000-35810200	Enhancers	Stomach Smooth Muscle	stomach
23	chr14:35807000-35810200	Enhancers	A549	lung
24	chr14:35807000-35810200	Weak transcription	HUVEC	blood vessel
25	chr14:35807000-35810400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr14:35807000-35810400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr14:35807000-35810400	Weak transcription	NH-A	brain
28	chr14:35807000-35810600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr14:35807000-35810600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr14:35807000-35810800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr14:35807200-35809600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr14:35807200-35810200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr14:35807200-35810400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr14:35807200-35810400	Weak transcription	Osteobl	bone
35	chr14:35807200-35810600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr14:35807200-35810600	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr14:35807400-35810000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr14:35807400-35810200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr14:35807400-35810200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr14:35807400-35810200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr14:35807400-35810200	Weak transcription	Brain Angular Gyrus	brain
42	chr14:35807400-35810200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr14:35807400-35810200	Weak transcription	Right Atrium	heart
44	chr14:35807400-35810400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr14:35807400-35810400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr14:35807400-35810400	Weak transcription	Psoas Muscle	Psoas
47	chr14:35807400-35810400	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr14:35807400-35810400	Weak transcription	NHDF-Ad	bronchial
49	chr14:35807400-35810600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr14:35807400-35810600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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